Nucleotide analogs

• US 5,656,745 A
• Filed: 09/17/1993
• Issued: 08/12/1997
• Est. Priority Date: 09/17/1993
• Status: Expired due to Term

• Current Assignee: Gilead Sciences Inc.
• Original Assignee: Gilead Sciences Inc.
• Inventors: Louie, Michael, Jones, Robert J., McGee, Lawrence R., Lin, Kuei-Ying, Prisbe, Ernest J., Arimilli, Murty, Bischofberger, Norbert
• Primary Examiner(s): Wilson, James O.
• Application Number:
  US08/123,483
• Time in Patent Office: 1,425 Days
• Field of Search: 530/330, 536/25.34, 536/27.14, 536/27.21, 536/27.6, 536/27.7, 536/27.8, 536/27.81, 536/28.2, 536/28.5, 536/28.51, 536/28.52, 536/28.53, 536/28.54 , 536/28.55, 544/242, 544/243, 544/244, 544/264, 544/265, 544/267, 544/303, 544/304, 544/310
• US Class Current: 536/25.34
• CPC Class Codes: C07F 9/6512 having the nitrogen atoms in positions 1 and 3
• CPC Class Codes: C07F 9/65616 containing the ring system having three or more than three double bonds between ring members or between ring members and non-ring members, e.g. purine or analogs
• CPC Class Codes: C07F 9/657181 the ring phosphorus atom and, at least, one ring oxygen atom being part of a (thio)phosphonic acid derivative
• CPC Class Codes: C07F 9/65742 non-condensed with carbocyclic rings or heterocyclic rings or ring systems
• CPC Class Codes: C07F 9/65744 condensed with carbocyclic or heterocyclic rings or ring systems
• CPC Class Codes: C07F 9/65785 the ring phosphorus atom and, at least, one ring sulfur atom being part of a thiophosphonic acid derivative
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 19/20 with the saccharide radical esterified by phosphoric or polyphosphoric acids

Abstract

Nucleotide analogs characterized by the presence of an amidate linked amino acid or an ester linked group which is bonded to the phosphorus atom of phosphonate nucleotide analogs are disclosed. The analogs comprise a phosphoamidate or ester bond that is hydrolyzed in vivo to yield a corresponding phosphonate nucleotide analog. Methods and intermediates for their synthesis and use are described.

Claims

1. A compound of the formula IIb ##STR23## wherein n is an integer having a value from 1 to 5 and if n>

1, each --C(R³)(R²)-- may be the same or different;

n1 is an integer;

R¹ is H or C₁ -C₉ alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N, COOR⁴ and halogen, C₃ -C₆ aryl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N, COOR⁴ and halogen or C₃ -C₉ aryl-alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N, COOR⁴ and halogen;

R² is independently H or C₁ -C₉ alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N, COOR⁴ and halogen, C₃ -C₆ aryl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N, COOR⁴ and halogen or C₃ -C₉ aryl-alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N, COOR⁴ and halogen;

R³ is independently C(O)--OR⁴, amino, C₁ -C₃ alkylamino, C₁ -C₃ alkyldiamino, C₁ -C₆ alkenylamino, hydroxy, thiol, C₁ -C₃ alkoxy, C₁ -C₃ alkthiol, (CH₂)_n COOR⁴, alkoxyphenyl, C₁ -C₆ alkyl, C₂ -C₆ alkenyl, C₆ -C₁₂ aryl which is substituted or unsubstituted with OH, halogen, SH, NH₂, phenyl, hydroxyphenyl or alkoxyphenyl;

R⁴ is H provided that n1 is greater than 1, or is C₃ -C₉ alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N and halogen, C₃ -C₆ aryl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N and halogen, C₃ -C₉ aryl-alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N and halogen;

Z is --CHR⁷ --R¹¹ --(CH₂)_m1 --C#(R⁸)((CH²)_m2 (R⁹))--(CH₂)_m3 --R¹⁰ --(CH₂)_m4 --, --O--C₆ H₄ --CH₂ --, --CHR⁷ --O--CHR⁷ --O--CHR⁷, --CHR⁷ --(CHR¹³)_m1 --CHR¹⁴ --R¹⁰ --, ##STR24## R⁷ is H or C₁ -C₄ alkyl;

R⁸ is H or C₁ -C₄ alkyl, C₂ -C₄ alkenyl, azidomethyl or azidoethyl;

R⁹ is halogen (F, Cl, Br or I), H or OH;

R¹⁰ is O, CH₂ or a chemical bond;

R¹¹ is O, S, CH₂, CHF, CF₂ ;

O is --C(R¹²)₂ --CH₂ --, --C(R¹²)--O--, --CR¹² ═

CR¹², or --C.tbd.C--, wherein each R¹² is independently H, or halogen;

R¹³ is H, halogen, OH, CH₃, CH₂ OH, or C₃ -C₁₂ acyloxymethyl;

R¹⁴ is independently H, halogen, OH, CH₃, CH₂ OH, C₃ -C₁₂ acyloxymethyl, or C_2-C12 acyloxy;

R²⁵ is CH₂, CHF or O;

R²⁶ is CH or S, provided that when R²⁵ is CH, R²⁶ is not S;

R²⁷ is H, OH, halogen, N₃, C₁ -C₄ alkoxy or when, R²⁶ is S, R²⁷ is absent;

R^27a is H, OH, halogen, N₃, C₁ -C₄ alkyl, C₁ -C₄ alkoxy;

R²⁸ is H, OH, halogen, N₃, C₁ -C₄ alkyl or C₁ -C₄ alkoxy;

R²⁹ is O, S, CH₂, CHF, CF₂ ;

R³² is O;

n2 is an integer having a value from 0 to 6;

m1 is an integer having a value from 0 to 4;

m2 is an integer having a value from 0 to 4;

m3 is an integer having a value from 0 to 4;

m4 is an integer having a value from 0 to 4;

the carbon atom designated C# is in the R, S or RS configuration; and

B is a base.

11. A compound of claim 1, wherein the compound is labeled with a detectable moiety selected from the group of an enzyme, radioisotope, stable free radical, fluorophor, and a chemiluminescent group.

14. The compound of claim 1 wherein n1 is 1 or 2.

2. A compound of the formula Ib ##STR25## wherein L¹ is an amino acid or polypeptide residue bonded to the phosphorus atom of the compound by an amidate bond and any carboxyl group that is linked by less than about 5 atoms to the amidate N is esterified or amidated;

X¹ is O or S;

the carbon atom designated # is in the R, S or RS configuration; and

B is a base.

3. The compound of claim 2 of the formula IIa ##STR26## wherein n is an integer having a value from 1 to 5 and if n>

1, each --C(R³)(R²)-- may be the same or different;

n1 is an integer;

R¹ is H or C₁ -C₉ alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N, COOR⁴ and halogen, C₃ -C₆ aryl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N, COOR⁴ and halogen or C₁ -C₉ aryl-alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N, COOR⁴ and halogen;

R² is independently H or C₁ -C₉ alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N, COOR⁴ and halogen, C₃ -C₆ aryl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N, COOR⁴ and halogen or C₃ -C₉ aryl-alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N, COOR⁴ and halogen;

R³ is independently C(O)--OR⁴, amino, C₁ -C₃ alkylamino, C₁ -C₃ alkyldiamino, C₁ -C₆ alkenylamino, hydroxy, thiol, C₁ -C₃ alkoxy, C₁ -C₃ alkthiol, (CH₂)_n COOR⁴, alkoxyphenyl, C₁ -C₆ alkyl, C₂ -C₆ alkenyl, C₆ -C₁₂ aryl which is substituted or unsubstituted with OH, halogen, SH, NH₂, phenyl, hydroxyphenyl or alkoxyphenyl; and

R⁴ is H provided that n1 is greater than 1, or is C₃ -C₉ alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N and halogen, C₃ -C₆ aryl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N and halogen, C₃ -C₉ aryl-alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N and halogen.

4. The compound of claim 3 wherein

n and n1 are 1;

R¹ is H, methyl, phenyl or benzyl;

R² is H;

R³ is H, --CH₃, --CH(CH₃)₂, --CH₂ --CH(CH₃)₂, --CHCH₃ --CH₂ --CH₃, --CH₂ --C₆ H₅, --CH₂ CH₂ --S--CH₃, --CH₂ OH, --CH(OH)--CH₃, --CH₂ --SH, --CH₂ -C₆ H₄ OH, --CH₂ --CO--NH₂, --CH₂ --CH₂ --CO--NH₂, --CH₂ --COOH, --CH₂ --CH₂ --COOH, --(CH₂)₄ --NH₂, --(CH₂)₃ --NH--C(NH₂)--NH₂, 1-guanidinoprop-3-yl, benzyl, 4-hydroxybenzyl, imidazol4-yl, indol-3-yl, methoxyphenyl or ethoxyphenyl; and

R⁴ is methyl, ethyl, propyl, isopropyl, butyl, t-butyl, phenyl, benzyl, 1-pyridyl, 3-pyridyl, 1-pyrimidinyl, pivaloyloxymethyl, N-ethylmorpholino, N-2-propylmorpholino, methoxyethyl, 4-N-methylpiperidyl, 3-N-methylpiperidyl, 2-, 3-, and 4-N,N-dimethylaminophenyl and 2-, 3-, and 4-N,N-diethylaminophenyl or 1-ethylpiperazinyl.

5. The compound of claim 4 wherein B is cytosin-1-yl, 6-azacytosin-1-yl, adenin-9-yl, guanin-9-yl or 2,6-diaminopurin-9-yl, and X¹ is O.

15. The compound of claim 3 wherein n1 is 1 or 2.

16. The compound of claim 15 wherein X¹ is oxygen.

17. The compound of claim 16 wherein L¹ is a naturally occurring amino acid.

18. The compound of claim 17 wherein R² is hydrogen and R³ is a side chain of the naturally occurring amino acid.

19. The compound of claim 18 wherein R³ is hydrogen, --CH₃, --CH(CH₃)₂, --CH₂ --CH(CH₃)₂, --CHCH₃ --CH₂ --CH₃, --CH₂ --C₆ t-IS, --CH₂ CH₂ --S--CH₃, --CH₂ OH, --CH(OH)--CH₃, --CH₂ --SH, --CH₂ --C₆ H₄ OH, --CH₂ --CO--NH₂, --CH₂ --CH₂ --CO--NH₂, --CH₂ --COOH, --CH₂ --CH₂ --COOH, --(CH₂)₄ --NH₂ or --(CH₂)₃ --NH--C(NH₂)--NH₂.

20. The compound claim 19 wherein B is cytosin-1-yl, 6-azacytosin-1-yl, adenin-9-yl, guanin-9-yl or 2, 6-diaminopurin-9-yl.

6. A compound of the formula Id ##STR27## wherein L¹ and L² are independently an amino acid or polypeptide residue bonded to the phosphorus atom of the nucleotide analog amidate by an amidate bond, or an oxyester, thioester, a substituted or unsubstituted amine, or hydroxy, provided that one or both of L¹ and L² is an amino acid or polypeptide residue and any carboxyl group that is linked by less than about 5 atoms to the amidate N is esterified or amidated:

Z is --CHR⁷ --R¹¹ --(CH₂)_m1 --C#(R⁸)((CH²)_m2 (R⁹))--(CH₂)_m3 --R¹⁰ --(CH₂)_m4 --, --O--C₆ H₄ --CH₂ --, --CHR⁷ --O--CHR⁷ --O--CHR⁷ --CHR⁷ --(CHR¹³)_m1 --CHR¹⁴ R¹⁰ --, ##STR28## R⁷ is H or C₁ -C₄ alkyl;

R⁸ is H or C₁ -C₄ alkyl, C₂ -C₄ alkenyl, azidomethyl or azidoethyl;

R⁹ is halogen (F, Cl, Br or I), H or OH;

R¹⁰ is O, CH₂ or a chemical bond;

R¹¹ is O, S, CH₂, CHF, CF₂ ;

O is --C(R¹²)₂ --CH₂ --, --C(R¹²)₂ --O--, --CR¹² ═

CR¹², or --C.tbd.C--, wherein each R¹² is independently H, or halogen;

R¹³ is H, halogen, OH, CH₃, CH₂ OH, or C₃ -C₁₂ acyloxymethyl;

R¹⁴ is independently H, halogen, OH, CH₃, CH₂ OH, C₃ -C₁₂ acyloxymethyl, or C₂ -C₁₂ acyloxy;

R²⁵ is CH₂, CHF or O;

R²⁶ is CH or S, provided that when R²⁵ is CH, R²⁶ is not S;

R²⁷ is H, OH, halogen, N₃, C₁ -C₄ alkyl, C₁ -C₄ alkoxy or when, R²⁶ is S, R²⁷ is absent;

R^27a is H, OH, halogen, N₃, C₁ -C₄ alkyl, C₁ -C₄ alkoxy;

R²⁸ is H, OH, halogen, N₃, C₁ -C₄ alkyl or C₁ -C₄ alkoxy;

R²⁹ is O, S, CH₂, CHF, CF₂ ;

R³² is O;

n2 is an integer having a value from 0 to 6;

m1 is an integer having a value from 0 to 4;

m2 is an integer having a value from 0 to 4;

m3 is an integer having a value from 0 to 4;

m4 is an integer having a value from 0 to 4;

the carbon atom designated C# is in the R, S or RS configuration; and

B is a base.

7. The compound of claim 6 wherein L¹ is of the formula III ##STR29## wherein L² is OR, SR or is the same as L¹ wherein, R is H,

C₃ -C₂₄ acyloxyalkyl,

C₆ -C₂₄ acyloxyarylalkyl,

C₃ -C₂₄ acyloxyalkoxyalkyl,

C₃ -C₂₄ acyloxyhaloalkyl, or

C₁ -C₂₀ alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N and halogen (F, Cl, Br, I),

C₃ -C₂₀ aryl which is unsubstituted or substituted by substituents independently selected from the group consisting of C₁ -C₆ alkyl, C₁ -C₆ alkoxy, C₁ -C₆ haloalkyl (1 to 3 halogen atoms), cyano, nitro, OH, O, N and halogen, or

C₄ -C₂₀ aryl-alkyl which is unsubstituted or substituted in the aryl moiety by substituents independently selected from the group consisting of C₁ -C₆ alkyl, C₁ -C₆ alkoxy, C₁ -C₆ haloalkyl (1 to 3 halogen atoms), cyano, nitro, OH, O, N and halogen.

8. The compound of claim 7 wherein

n and n1 are 1;

R is N-ethylmorpholino, pivaloyloxymethyl, phenyl, benzyl, isopropyl, t-butyl, ethyl, isopropyl, butyl, adamantoyloxymethyl, 3-methoxyphenyl, 2-carboethoxyphenyl, 4-fluorophenyl, 2,4-difluorophenyl, 3,5-dimethoxyphenyl, 2,4-dichlorophenyl, 2-ethoxyphenyl, 3-dimethylaminophenyl, 4-trifluoromethylbenzyl, 2-ethylsalicyl, --O--CH₂ --O--C(O)--C₁₀ H₁₆, --C₆ H₄ --CH₂ --N(CH₃)₂, --CH₂ --CH₂ F, --CH₂ --CH₂ Cl, --CH₂ --CF₃, --CH₂ --CCl₃, R⁵, NHR⁶ or N(R⁶)₂

wherein,

R⁵ is CH₂ C(O)N(R⁶)₂, CH₂ C(O)OR⁶, CH₂ OC(O)R⁶, CH(R⁶)OC(O)R⁶, CH₂ C(R⁶)₂ CH₂ OH, or CH₂ OR⁶, and R⁶ is C₁ -C₂₀ alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N and halogen (1 to 5 halogen atoms), C₆ -C₂₀ aryl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N and halogen (1 to 5 halogen atoms) or C₇ -C₂₀ aryl-alkyl which is unsubstituted or substituted by substituents independently selected from the group consisting of OH, O, N and halogen (1 to 5 halogen atoms);

R¹ is H, methyl, ethyl, isopropyl, phenyl or benzyl;

R² is H;

R³ is H, --CH₃, --CH(CH₃)₂, --CH₂ --CH(CH3₂, --CHCH₃ --CH₂ --CH₃, --CH₂ --C₆ H₅, --CH₂ CH₂ --S--CH₃, --CH₂ OH, --CH(OH)--CH₃, --CH₂ --SH, --CH₂ -C₆ H₄ OH, --CH₂ --CO--NH₂, --CH₂ --CH₂ --CO--NH₂, --CH₂ --COOH, --CH₂ --CH₂ --COOH, --(CH₂)₄ --NH₂, --(CH₂)₃ --NH--C(NH₂)--NH₂, 1-guarddinoprop-3-yl, benzyl, 4-hydroxybenzyl, imidazol-4-yl, indol-3-yl, methoxyphenyl or ethoxyphenyl; and

R⁴ is methyl, ethyl, propyl, isopropyl, butyl, t-butyl, phenyl, benzyl, 1-pyridyl, 3-pyridyl, 1-pyrimidinyl, pivaloyloxymethyl, N-ethylmorpholino, N-2-propylmorpholino, methoxyethyl, 4-N-methylpiperidyl, 3-N-methylpiperidyl, 2-, 3-, and 4-N,N-dimethylaminophenyl and 2-, 3-, and 4-N,N-diethylaminophenyl or 1-ethylpiperazinyl.

9. The compound of claim 8 wherein Z is --CHR⁷ --R¹¹ --(CH₂)_m1 --C(R⁸)((CH₂)_m2 (R⁹))--(CH₂)_m3 --R¹⁰ --(CH₂)_m4 --, ##STR30##

10. The compound of claim 9 wherein

Z is --CH₂ --O--CH₂ --CH₂ --, --CH₂ --O--CH₂ --CH(CH₂ OH)--, --CH₂ --O--CH₂ --CH(CH₂ F)--, --CH₂ --O--CH₂ --CH(CH₃)--, --CH₂ --O--CH₂ --CH(CH=CH₂)- or --CH₂ --O--CH₂ --CH(CH₂ N₃)--, or is of formula IV or V ##STR31## wherein R²⁵ and R²⁹ are O;

R²⁶ is CH;

R²⁷ and R²⁸ are H; and

B is adenin-9-yl, 1-deazaadenin-9-yl, 3-deazaadenin-9-yl, 7-deaza-8-azaadenin-9-yl, 8-azaadenin-9-yl, guanin-9-yl, 2, 6-diaminopurin-9-yl, 2-aminopurin-9-yl, thymin-1-yl, cytosin-1-yl, 5-fluorocytosin-1-yl, 6-azacytosin-1-yl, 5-methylcytosin-1-yl, 5-bromovinyluracil-1-yl, 5-fluorouracil-yl or 5-trifluoromethyluracil-1-yl.

12. The compound of claim 7 wherein L² is the same as L¹.

13. The compound of claim 12 wherein

B is adenin-9-yl, guanin-9-yl, cytosin-1-yl, 2,6-diaminopurin-9-yl, 2-aminopurin-9-yl, 6-azacytosin-1-yl, 1-deazaadenin-9-yl, 3-deazaadenin-9-yl, 8-azaadenin-9-yl or 7-deaza-8-azaadenin-9-yl;

Z is --CH₂ --O--CH₂ --CH₂ --, --CH₂ --O--C#H(CH₂ --OR⁴)--CH₂ -- or --CH₂ --O--C#H(CH₃)--CH₂ --;

L¹ is --NH--CH(CH(CH₃)₂)--C(O)--OR⁴, --NH--CH(CH₃)(CH₃)₂)--C(O)--OR⁴, --NH--CH(CH₂ --C₆ H₅)--C(O)--OR⁴, --NH--CH(CH₂ --C₆ H₄ OH)--C (O)--OR⁴, --NH--CH(CH(OH)(CH₃)--C(O)--OR⁴, --NH--CH(CH₂ CH₂ CH₂ NH₂)--CH₂ --C(O)--OR⁴, --NH--CH(CH₂ CH₂ CH₂ CH₂ NH₂)--CH₂ --C(O)--OR⁴, --NH--CH(CH₂ CH₂ C(O)OR⁴)--C(O)--OR⁴ or --NH--CH(CH₃)₂)--CH₂ --C(O)--C)R₄ ; and

R⁴ is hydrogen, methyl, ethyl, propyl, isopropyl, butyl, t-butyl, phenyl, benzyl, 1-pyridinyl, 3-pyridyl, 1-pyrimidinyl, pivaloyloxymethyl, N-ethylmorpholino, N-2-propylmorpholino, methoxyethyl, 4-hydroxy-N-methylpiperidinyl, 4-N-methylpiperidyl, 3-N-methylpiperidyl, 2-N,N-dimethylaminophenyl, 3-N,N-dimethylaminophenyl, 4-N,N-dimethylaminophenyl and 2-N,N-diethylaminophenyl, 3-N,N-diethylaminophenyl, 4-N,N-diethylaminophenyl, 1-ethylpiperazinyl, 3-hydroxy-N-methylpiperidinyl or 1-ethylpiperazinyl.

21. The compound of claim 7 wherein n1 is 1 or 2.

22. The compound of claim 21 wherein L² and L¹ are a naturally occurring amino acid.

23. The compound of claim 22 wherein L¹ and L² are the same.

24. The compound of claim 23 wherein R² is hydrogen and R³ is a side chain of the naturally occuring amino acid.

25. The compound of claim 24 wherein R³ is hydrogen, --CH₃, --CH(CH₃)₂, --CH₂ --CH(CH₃)₂, --CHCH₃ --CH₂ --CH₃, --CH₂ --C₆ H₅, --CH₂ CH₂ --S--CH₃, --CH₂ OH, --CH(OH)--CH₃, --CH₂ --SH, --CH₂ --C₆ H₄ OH, --CH₂ --CO--NH₂, --CH₂ --CH₂ --CO--NH₂, --CH₂ --COOH, --CH₂ --CH₂ --COOH, --(CH₂)₄ --NH₂ or --(CH₂)₃ --NH--C(NH₂)--NH₂.

26. The compound claim 25 wherein Z is --CH₂ --O--CH₂ --CH₂ --, --CH₂ --O--CH₂ --CH(CH₂ OH)--, --CH₂ --O--CH₂ --CH(CH₃)--, or ##STR32##

27. The compound claim 26 wherein Z is --CH₂ --O--CH₂ --CH₂ --, --CH₂ --O--CH₂ --CH(CH₂ OH)--, or --CH₂ --O--CH₂ --CH(CH₃)--.

28. The compound claim 27 wherein B is adenin-9-yl, 1-deazaadenin-9-yl, 3-deazaadenin-9-yl, 7-deaza-8-azaadenin-9-yl, 8-azaadenin-9-yl, guanin-9-yl, 2,6-diaminopurin-9-yl, 2-aminopurin-9-yl, thymin-1-yl, cytosin-1-yl, 5-fluorocytosin-1-yl, 6-azacytosin-1-yl, 5-methylcytosin-1-yl, 5-bromovinyluracil-1-yl, 5-fluorouracil-1-yl or 5-trifluoromethyluracil-1-yl.

29. The compound of claim 28 wherein B is adenin-9-yl, guanin-9-yl, or cytosin-1-yl.